The C.I.D. investigators that have been dispatched to the squadron are convinced that the Chaplain has been intercepting Major Major Major Major's mail and signing documents Washington Irving or Irving Washington. Yossarian has been abusing his duty of censoring letters sent home by the enlisted men, and signing those names to the letters he vandalises, except once where he signs "I yearn for you tragically. A. T. Tappman, Chaplain, U.S. Army". (Note that Yossarian's duties involve censoring enlisted men's letters; the chaplain is an officer.) This vandalism brings the C.I.D. down to the base.
Later on, Major Major Major Major begins signing those names to official documents, after he discovers that when he does, he never sees them again. Before they would always return with more attached documents to deal with.
These suspected acts of protest result in the Chaplain being interrogated at length by the C.I.D. investigators in the final chapters of the book. They find him guilty of all his "crimes"; since they're his crimes, he must have committed them. They also find him guilty of all the charges against him that they haven't thought of yet. Then they release him. This is actually worse than being jailed, because he never knows when he will be grabbed again.
When Yossarian tells the Chaplain that someone came into his hospital room to torment him with the words "We've got your pal!", the Chaplain replies "Well, I'm your pal and they've certainly got me." At the end of the novel, all Yossarian's other friends are dead, or, like Doc Daneeka, reduced to bureaucratic zombies. Only the Chaplain remains, and he has definitely been got (although in the last paragraphs he announces his intent to "stay here and persevere").
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